Variant chrX-8184147-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000659022.1(ENSG00000285679):n.972-44188A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.328 in 111,693 control chromosomes in the GnomAD database, including 5,203 homozygotes. There are 10,926 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.33 ( 5203 hom., 10926 hem., cov: 24)

Consequence

ENST00000659022.1 intron, non_coding_transcript

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.325

Variant links:

Genes affected

(HGNC:):

links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.01).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.574 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect
LOC107985675	XR_001755783.2 linkuse as main transcript	n.1915-44188A>G	intron_variant, non_coding_transcript_variant
LOC107985675	XR_001755782.2 linkuse as main transcript	n.1915-44188A>G	intron_variant, non_coding_transcript_variant
LOC107985675	XR_001755784.2 linkuse as main transcript	n.1915-44188A>G	intron_variant, non_coding_transcript_variant
LOC107985675	XR_007068387.1 linkuse as main transcript	n.1915-44188A>G	intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000659022.1 linkuse as main transcript	n.972-44188A>G		intron_variant, non_coding_transcript_variant
	ENST00000649338.1 linkuse as main transcript	n.263-44188A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.328

AC:

36586

AN:

111636

Hom.:

5206

Cov.:

AF XY:

0.321

AC XY:

10871

AN XY:

33876

show subpopulations

Gnomad AFR

AF:

0.552

Gnomad AMI

AF:

0.101

Gnomad AMR

AF:

0.333

Gnomad ASJ

AF:

0.240

Gnomad EAS

AF:

0.595

Gnomad SAS

AF:

0.274

Gnomad FIN

AF:

0.199

Gnomad MID

AF:

0.326

Gnomad NFE

AF:

0.205

Gnomad OTH

AF:

0.320

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.328

AC:

36642

AN:

111693

Hom.:

5203

Cov.:

AF XY:

0.322

AC XY:

10926

AN XY:

33943

show subpopulations

Gnomad4 AFR

AF:

0.552

Gnomad4 AMR

AF:

0.334

Gnomad4 ASJ

AF:

0.240

Gnomad4 EAS

AF:

0.595

Gnomad4 SAS

AF:

0.272

Gnomad4 FIN

AF:

0.199

Gnomad4 NFE

AF:

0.205

Gnomad4 OTH

AF:

0.328

Alfa

AF:

0.233

Hom.:

13160

Bravo

AF:

0.359

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

1.0

DANN

Benign

0.40

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over